Fix regarding expected behavior of diff when finding image size

.gitignore

@@ -1,5 +1,7 @@
+*~
 *.m~
 *.asv
 *.DS_Store
 *.swp
 
+wiki

README.md

@@ -2,7 +2,14 @@
 
 VISTASOFT is the main software repository of the [Vista lab](http://vistalab.stanford.edu) at [Stanford University](http://stanford.edu). It contains Matlab code to perform a variety of analysis on MRI data, including functional MRI and diffusion MRI.
 
-It has the following modules:
+### License
+
+(c) Vista lab, Stanford University.
+
+Unless otherwise noted, all our code is released under the [GPL](http://www.gnu.org/copyleft/gpl.html) 
+
+### Modules
+Vistasoft contains the following modules:
 
 - mrAlign : Aligning functional and anatomical data
 - mrAnatomy: Handling anatomical MRI data. 
@@ -16,23 +23,43 @@ And in addition:
 - utilities
 - setup
 - tutorials 
-- external: functions written by others that we use as dependencies (see optional software).
+- external: functions written by others that we use as dependencies (see optional packages).
 
-External dependencies:
+### External dependencies
+Vistasoft depends on the following packages:
 - [Matlab](http://mathworks.com)
+  - The code has been validated for Matlab 2014b (8.4) - Matlab 2017b (9.3)
 - [SPM](http://www.fil.ion.ucl.ac.uk/spm/)
 
-Optional packages:
+### Optional Packages
  - [Freesurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)
  - [FSL](http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
  - [MRTrix](http://www.nitrc.org/projects/mrtrix/)
  - [JSONLab](http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?jsonlab)
+ - [RemoteDataToolbox](https://github.com/isetbio/RemoteDataToolbox)
 
+### Documentation
 For detailed documentation, please visit the [VISTA lab wiki](http://vistalab.stanford.edu/wiki).
 
+### Installation
 
-For help with the new mrInit intialization method, please see the [Initialization Page](http://white.stanford.edu/newlm/index.php/Initialization#mrInit).
+To install Vistasoft:
 
-(c) Vista lab, Stanford University.
+1. Clone the Vistasoft repository on your local machine; for example:
+
+   ```sh
+   > cd ~/matlab
+   > git clone https://github.com/vistalab/vistasoft
+
+   ```
+
+2. Start Matlab and Add the Vistasoft repository's base directory to your Matlab path:
+
+   ```matlab
+   addpath(genpath('~/matlab/vistasoft'));
+   ```
+
+   Note that if you have installed additional Matlab packages (such as the RemoteDataToolbox), you will have to ensure that these packages are on your path as well.
+
+For help with the new mrInit intialization method, please see the [Initialization Page](http://white.stanford.edu/newlm/index.php/Initialization#mrInit).
 
-Unless otherwise noted, all our code is released under the [GPL](http://www.gnu.org/copyleft/gpl.html) 

external/brainbrowser/fg2MNIObj.m

@@ -0,0 +1,121 @@
+function [coords, lineList, startPoints] = fg2MNIObj(fg,varargin)
+% FG2MNIOBJ - Convert array of fg to MNI Obj file for visualization
+%
+% Required Inputs
+%   fg:  An array of vistasoft fiber groups
+% Optional inputs
+%  fname:      Full path to output file name
+%  overwrite:  Overwrite existing file
+%  jitter:     Jitter the RGB colors by this random amount (0,1)
+%
+%  You can view the MNI OBJ data in brainbrowser by loading the file to
+%  this site:  https://brainbrowser.cbrain.mcgill.ca/surface-viewer#dti
+%
+% See also: obj<> files.  Perhaps this should be grouped with those, but I
+% am not sure this format is viewable by meshlab.app, and a legitimate OBJ
+% file.
+%
+%
+% RF/BW, Vistasoft Team 2016
+
+%% Parse file name and other parameters that may arise
+p = inputParser;
+
+p.addRequired('fg');
+p.addParameter('fname','test.mni.obj',@ischar);  % Output file
+p.addParameter('overwrite',false);               % Forces overwrite
+p.addParameter('jitter', 0.1);                  % Jitter the colors
+
+p.parse(fg,varargin{:});
+fname     = p.Results.fname;
+overwrite = p.Results.overwrite;
+jitter    = p.Results.jitter;
+
+%%
+nFibers = 0;
+nGroups = length(fg);
+for ii=1:nGroups, nFibers = nFibers + length(fg(ii).fibers); end
+
+color = zeros(nFibers,4);     % Initialize a color for each group
+nPoints = zeros(nFibers,1);   % How many points in each fiber?
+
+kk = 0;
+for ff = 1:nGroups
+    for jj=1:length(fg(ff).fibers)
+        kk = kk + 1;
+        color(kk,:) = [fg(ff).colorRgb/255,1];
+        nPoints(kk)  = size(fg(ff).fibers{jj},2);
+    end
+end
+
+fgAll = fg(1);
+for ff = 2:nGroups
+    fgAll = fgMerge(fgAll,fg(ff),'all');
+end
+
+%% Store the coords and list of points in each line
+coords = zeros(sum(nPoints),3);
+startPoints = [0; cumsum(nPoints)];
+lineList = cell(1,nFibers);
+for ii=1:nFibers
+    lineList{ii} = (startPoints(ii)+1):startPoints(ii+1);
+    coords(lineList{ii},:) = fgAll.fibers{ii}';
+end
+
+%% Open the file for writing
+
+if exist(fname,'file') && ~overwrite
+    disp('The file already exists.  Press space bar to over-write');
+    pause
+end
+
+% We should probably test if the file exists already!
+fileID = fopen(fname,'w');
+fprintf(fileID,'L 1 %d\n', size(coords,1));
+
+% Write out the coords
+fprintf(fileID,'%.4f %.4f %.4f\n',coords');
+
+% Write the color of all the lines.
+% We need to figure out how to do each line, or ...
+% And this should become a parameter
+% And we should figure out what the 0 at the front means.  Renzo knows, and
+% it is important.
+% The others are R G B alpha
+nLines = length(lineList);
+fprintf(fileID,'\n%d\n',nLines);
+
+% Jitter the color for each line
+% Make some random numbers to add to the color
+randColors = color;
+if jitter > 0
+    theseColors = randColors(:,1:3);
+    scale = mean(theseColors,2);
+    randFactor = 1 + randn(size(scale))*jitter;
+    theseColors = diag(randFactor)*theseColors ;
+    randColors = [theseColors,ones(nFibers,1)];
+    randColors = min(randColors,1);
+    randColors = max(randColors,0);
+end
+
+fprintf(fileID,'1\n');
+for ii=1:nLines
+    fprintf(fileID,'%.2f %.2f %.2f %.2f\n',...
+        randColors(ii, 1),randColors(ii, 2),randColors(ii, 3),randColors(ii, 4));
+end
+% In principle, we could have '2\n' and then a color per vertex
+
+% Now a list that counts the number of points in each fiber.
+fprintf(fileID,'%d ',startPoints(2:end));
+fprintf(fileID,'\n\n');
+
+% Write out the lineLists (points in each line)
+for ii=1:nFibers
+    fprintf(fileID,'%d ',lineList{ii}-1);
+    fprintf(fileID,'\n');
+end
+
+% Close the file and go home
+fclose(fileID);
+
+end

external/dirwalk/dirwalk.m

@@ -0,0 +1,202 @@
+function varargout = dirwalk(topPath, visitor, varargin)
+%DIRWALK Generate the file names in a directory tree by walking the tree
+%
+% Description:
+%   Function DIRWALK generates the file names in a directory tree by walking the tree 
+%   top-down. For each directory in the tree rooted at directory topPath.
+%   For each directory of tree you can call "Visitor Function" for files processing.
+%
+%
+% Using:
+%   [pathNames, dirNames, fileNames] = dirwalk(topPath)
+%   dirwalk(topPath, visitor)
+%   dirwalk(topPath, visitor, varargin)
+%   varargout = dirwalk(topPath, visitor, varargin)
+%   [visitorOutput1, visitorOutput2, ..., visitorOutputN] = dirwalk(topPath, visitor)
+%   [...] = dirwalk(topPath, visitor, visitorInput1, visitorInput2, ..., visitorInputN)
+%   [...] = dirwalk(topPath, visitor, varargin)
+%
+%
+% Input:
+%   topPath -- (Required) Top path name (Root path name)
+%
+%   visitor -- (Optional) Function handle. The function will be called 
+%                         when visiting each directory of tree. 
+%
+%   Signatures of visitor function: 
+%   	visitor(pathName, DirListing)
+%       visitor(pathName, DirListing, in1, in2, ..., inN)
+%       visitor(pathName, DirListing, varargin)
+%       varargout = visitor(...)
+%      	[out1, out2, ..., outN] = visitor(...)
+%       
+%   Input arguments:
+%       pathName   -- (Required) Path to visited directory. String.
+%                                (passed within DIRWALK)
+%
+%       DirListing -- (Required) Visited directory listing. 
+%                                Array of structs output of function DIR. 
+%                                (passed within DIRWALK)
+%
+%       varargin   -- (Optional) Other input arguments. (Passed outside)
+%
+%
+% Output:
+%   dirPaths  -- (Default visitor output) Visited path names. Cell array of strings.
+%   dirNames  -- (Default visitor output) Directory names in visited paths (without '.' and '..'). Cell array of cell arrays.
+%   fileNames -- (Default visitor output) File names in visited paths. Cell array of cell arrays.
+%   visitorOutputs -- Visitor function outputs 
+%
+%
+% Examples:
+%   topPath = fullfile(matlabroot, 'toolbox', 'matlab', 'demos');
+%
+%   [pathNames, dirNames, fileNames] = dirwalk(topPath);
+%   
+%   dirwalk(topPath, @(y,x) disp(strcat(y, filesep, {x.name}')))
+%
+%
+% See Also DIR, LS
+%
+
+% -------------------------------------------------------------------------
+%   Version   : 1.1
+%   Author    : Evgeny Pr aka iroln <[email protected]>
+%   Created   : 10.10.10
+%   Updated   : 03.07.11
+%
+%   Copyright : Evgeny Prilepin (c) 2010-2011
+% -------------------------------------------------------------------------
+
+error(nargchk(1, Inf, nargin));
+
+if (nargin < 2)
+    error(nargoutchk(0, 3, nargout));
+
+    visitor = @default_visitor;
+    visitorNumOutputs = 3;
+    isUseDefaultVisitor = true;
+else
+    visitorNumOutputs = nargout;
+    isUseDefaultVisitor = false;
+end
+
+validateattributes(topPath, {'char'}, {'row'}, ...
+    mfilename('fullpath'), '"Top Path Name"', 1)
+
+if ~isempty(visitor)
+    validateattributes(visitor, {'function_handle'}, {'scalar'}, ...
+        mfilename('fullpath'), '"Visitor Function Handle"', 2)
+end
+
+varargout = dir_tree_helper(topPath, ...
+    visitor, visitorNumOutputs, isUseDefaultVisitor, varargin{:});
+%--------------------------------------------------------------------------
+
+%==========================================================================
+function visitorOutputs = dir_tree_helper(topPath, visitorHandle, ...
+    visitorNumOutputs, isUseDefaultVisitor, varargin)
+%DIR_TREE_HELPER Helper function for get directory tree
+
+% Allocate memory for tree listing
+preallocDirItems = 100000;
+outputs = cell(preallocDirItems, visitorNumOutputs);
+counter = 1;
+
+% Get tree listing
+[counter, outputs] = dir_tree_listing(topPath, counter, outputs, ...
+    visitorHandle, visitorNumOutputs, isUseDefaultVisitor, varargin{:});
+
+% Remove extra
+if (counter < preallocDirItems)
+    outputs(counter+1:end, :) = [];
+end
+
+% Construct visitor function outputs
+visitorOutputs = cell(1, visitorNumOutputs);
+for i = 1:visitorNumOutputs
+    visitorOutputs(i) = {outputs(:,i)};
+end
+%--------------------------------------------------------------------------
+
+%==========================================================================
+function [counter, outputs] = dir_tree_listing(topPath, counter, outputs, ...
+    visitorHandle, visitorNumOutputs, isUseDefaultVisitor, varargin)
+%DIR_TREE_LISTING Generate dir tree listing
+
+% Get listing of current directory
+Listing = dir(topPath);
+
+% Call Visitor function
+visitorOutputs = visitor_call_helper(topPath, Listing, ...
+    visitorHandle, visitorNumOutputs, varargin{:});
+
+if isUseDefaultVisitor
+    dirNames = visitorOutputs{2};
+else
+    dirNames = get_dir_file_names(Listing);
+end
+
+if (visitorNumOutputs > 0)
+    outputs(counter,:) = visitorOutputs;
+end
+
+% Recursive walking directories in current directory
+for i = 1:length(dirNames)
+    nextRootPath = fullfile(topPath, dirNames{i});
+
+    [counter, outputs] = dir_tree_listing(nextRootPath, counter+1, outputs, ...
+        visitorHandle, visitorNumOutputs, isUseDefaultVisitor, varargin{:});
+end
+%--------------------------------------------------------------------------
+
+%==========================================================================
+function visitorOutputs = visitor_call_helper(topPath, Listing, ...
+    visitor, numOutputs, varargin)
+%VISITOR_CALL_HELPER Helper function for call visitor function
+
+if (numOutputs == 0)
+    % Visitor function without output arguments
+    visitorOutputs = {};
+    visitor(topPath, Listing, varargin{:});
+else
+    % Construct eval command for call visitor function with any number output arguments
+    outputNumbers = num2cell(1:numOutputs);
+
+    %FIXME: It is not recommended, but otherwise doesn't work
+    outputArgs = deblank(sprintf('outputs{%d} ', outputNumbers{:}));
+    visitorCalling = sprintf('[%s] = visitor(topPath, Listing, varargin{:});', outputArgs);
+    eval(visitorCalling);
+
+    visitorOutputs = outputs;
+end
+%--------------------------------------------------------------------------
+
+%==========================================================================
+function [pathName, dirNames, fileNames] = default_visitor(rootPath, Listing)
+%DEFAULT_VISITOR Default Visitor function
+%
+% Default visitor function return 3 output arguments:
+%   pathNames -- visited paths names
+%   dirNames  -- Directories names in visited directories
+%   fileNames -- Files names in visited directories
+%
+
+pathName = rootPath;
+[dirNames, fileNames] = get_dir_file_names(Listing);
+%--------------------------------------------------------------------------
+
+%==========================================================================
+function [dirNames, fileNames] = get_dir_file_names(Listing)
+%GET_DIR_FILE_NAMES 
+
+names = {Listing.name}';
+isDirs = [Listing.isdir];
+dirNames = names(isDirs);
+fileNames = names(~isDirs);
+
+% Exclude special directories '.' and '..'
+inds = ~strcmp(dirNames, '.') & ~strcmp(dirNames, '..');
+dirNames = dirNames(inds);
+%--------------------------------------------------------------------------
+